[Bioperl-l] entrezgene binary ASN

[Stefan Kirov]

Michael,
What if gene2xml fails (incomplete downloads, etc.)? I would prefer to 
keep it separate, but I see some people would prefer your way. My 
intention was not to rewrite the parser- it should work fine on the 
converted ags file. Thanks for the contribution!
Stefan

Michael Seewald wrote:

>
> Hi Stefan,
>
> The most convenient way would be to open it as a pipe:
>
> my $parser = Bio::ASN1::EntrezGene->new('file' => "gene2xml -i 
> Homo_sapiens.ags.gz -c -x -b | ");
> while(my $result = $parser->next_seq) {
> #...
> }
>
> It may be actually faster than before, because you save disk I/O. And 
> even better, there is no need to rewrite the parsers.
>
> Best wishes,
> Michael
>
>
> On 9/16/05, *Stefan Kirov* <skirov at utk.edu <mailto:skirov at utk.edu>> 
> wrote:
>
>     NCBI provides now only the binary ASN format. Entrezgene parser
>     will not
>     parse it, but you can convert with gene2xml:
>
>     RT - Shiryayev, Sergey (NIH/NLM/NCBI) wrote:
>
>
>     >>Stefan,
>     >>
>     >>Try this:
>     >>
>     >>./gene2xml -i All_Data.ags.gz -c -x -b | more
>     >>
>     >>
>     >>Sergey Shiryayev
>     >>NCBI Contractor
>     >
>     Note that you shoul proceed the gzipped file.
>     Stefan
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>
>
> -- 
> Dr. Michael Seewald
> Bioinformatics
> Bayer HealthCare AG


-- 
Stefan Kirov, Ph.D.
University of Tennessee/Oak Ridge National Laboratory
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e-mail: skirov at utk.edu
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